title: Genome-wide study of NAGNAG alternative splicing in Arabidopsis.
abstract: NAGNAG alternative splicing is one type of alternative splicing in mammals and plants. There are two opposite arguments regarding the mechanism of this NAGNAG event, i.e. whether splice variation is controllable by the cell or is just biological noise. In this paper, we systematically investigated NAGNAG acceptors in Arabidopsis thaliana using both cDNA/EST and RNA-Seq data. We identified 9,473 NAGNAG motifs, including 529 cDNA/EST-confirmed NAGNAG acceptors. A nomenclature tree for this type of alternative splicing was defined based on the cDNA/EST validation, location in the exon, sequence and expression level. Low expression of some NAGNAG motifs was observed in various tissues or pathogen-infected samples, indicating the existence of background splicing. Tissue-specific or treatment-specific differences in the dynamic profiles suggest that some NAGNAG acceptors are highly regulated.
authors.affiliation: College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, Shandong, People's Republic of China.
authors.forename: Yanjing
authors.initials: Y
authors.lastname: Shi
authors.forename: Guangli
authors.initials: G
authors.lastname: Sha
authors.forename: Xiaoyong
authors.initials: X
authors.lastname: Sun
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D017398:Alternative Splicing; D017360:Arabidopsis / Q000235:genetics* / Q000382:microbiology; D005091:Exons; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D022821:RNA Splice Sites
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D022821:RNA Splice Sites